Mass spectrometry data on specialized metabolome of medicinal plants used in East Asian traditional medicine

Abstract

Traditional East Asian medicine not only serves as a potential source of drug discovery, but also plays an important role in the healthcare systems of Korea, China, and Japan. Tandem mass spectrometry (MS/MS)-based untargeted metabolomics is a key methodology for high-throughput analysis of the complex chemical compositions of medicinal plants used in traditional East Asian medicine. This Data Descriptor documents the deposition to a public repository of a re-analyzable raw LC-MS/MS dataset of 337 medicinal plants listed in the Korean Pharmacopeia, in addition to a reference spectral library of 223 phytochemicals isolated from medicinal plants. Enhanced by recently developed repository-level data analysis pipelines, this information can serve as a reference dataset for MS/MS-based untargeted metabolomic analysis of plant specialized metabolites.

Open Access Repository-Scale Propagated Nearest Neighbor Suspect Spectral Library for Untargeted Metabolomics

“…Several flavonoid diglycosides containing pentoses and hexoses were detected using MS/MS spectral library searching, with the default GNPS libraries providing ten spectrum annotations in this molecular family and the suspect library contributing annotations for 27 diglycoside analogs ( Supplementary Figure 6 ). 30 Visual inspection of the MS/MS spectra indicated several modifications to formulate structural hypotheses for these suspects. For example, the apigenin-8- C -hexosylhexoside suspect with a delta mass of -30.019 Da corresponds to apigenin-8- C -pentosylhexoside.…”

“…Investigation of suspects from a dataset of medicinal plants listed in the Korean Pharmacopeia. 30 a. Flavonoids cluster in a molecular network created from the Korean Pharmacopeia medicinal plants dataset. The reference library hits are shown by the blue squares.…”

A Sample-Centric and Knowledge-Driven Computational Framework for Natural Products Drug Discovery

“…To illustrate the potential of our approach to organize and interrogate heterogeneous data sets, we have further formatted and integrated a publicly available metabolomics data set of 337 Korean medicinal plants acquired under different experimental conditions in the ENPKG. 24 Here, we will first detail the workflow structure and its technical aspects and then show how the KG structure can help answer research questions and lead to the identification of new anti-T. cruzi and anti-L. donovani compounds. We finally discuss the current limitations of the workflow and future improvements.…”

Small molecule metabolites: discovery of biomarkers and therapeutic targets

“…High-throughput metabolomics agrees with holistic view and insight into a comprehensive mechanistic efficacy of herbal medicines, including medicinal plants, preparation, active compounds, aqueous extracts and formulas or patent medicines. 719 – 723 Target small molecule metabolite based-screens offer numerous advantages for functional ingredients discovery from natural products as a treasure trove for drug development, and allows in-depth understanding of the possible targets and action mechanisms. Advanced metabolomics techniques consist of LC-MS, NMR, and GC-MS in combination with pattern recognition analysis or multivariate statistical analyses could identify a large number of metabolites and impact on diagnosing disease, discovery of biomarkers, investigation of phenotypes, classify physiological status and response to treatment, unravel efficacy of metabolic-targeting drug, cover the full pipeline of lead compound discovery and development from medicinal plants.…”

“…Advanced metabolomics techniques consist of LC-MS, NMR, and GC-MS in combination with pattern recognition analysis or multivariate statistical analyses could identify a large number of metabolites and impact on diagnosing disease, discovery of biomarkers, investigation of phenotypes, classify physiological status and response to treatment, unravel efficacy of metabolic-targeting drug, cover the full pipeline of lead compound discovery and development from medicinal plants. 719 , 724 – 727 Based on multiple metabolic alterations involved in disease pathogenesis, it is particularly pivotal to explore herb-derived bioactive ingredients for these mechanistic basis, damaged metabolic pathways and therapeutic targets of metabolic diseases. Moreover, herb-derived bioactive ingredients have been screened and validated in vitro and in vivo, to investigate the underlying changes of small metabolites and metabolic pathways, and to find potential targets (Fig.…”